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- PDB-6iaw: Structure of head fiber and inner core protein gp22 of native bac... -

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Basic information

Entry
Database: PDB / ID: 6iaw
TitleStructure of head fiber and inner core protein gp22 of native bacteriophage P68
Components
  • Arstotzka protein
  • Head fiber
  • Major head protein
  • inner core protein
KeywordsSTRUCTURAL PROTEIN / bacteriophage / head fiber / inner core protein
Function / homologyUncharacterized protein / Major head protein
Function and homology information
Biological speciesStaphylococcus phage P68 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHrebik, D. / Skubnik, K. / Fuzik, T. / Plevka, P.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization3041 Czech Republic
16-29916A Czech Republic
CitationJournal: Sci Adv / Year: 2019
Title: Structure and genome ejection mechanism of phage P68.
Authors: Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka /
Abstract: Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect ...Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.
History
DepositionNov 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-4440
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major head protein
B: Major head protein
C: Major head protein
J: Arstotzka protein
I: Arstotzka protein
D: Arstotzka protein
E: Arstotzka protein
H: Head fiber
M: Major head protein
N: Major head protein
O: Major head protein
Q: Arstotzka protein
S: Arstotzka protein
L: Head fiber
X: inner core protein
Y: inner core protein
Z: inner core protein
K: Head fiber


Theoretical massNumber of molelcules
Total (without water)350,94618
Polymers350,94618
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area67600 Å2
ΔGint-332 kcal/mol
Surface area130550 Å2
MethodPISA

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Components

#1: Protein
Major head protein


Mass: 46954.941 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I3
#2: Protein
Arstotzka protein


Mass: 6922.464 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I2
#3: Protein Head fiber


Mass: 5720.042 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: Poly alanine chain fitted to the density of head-fiber
Source: (natural) Staphylococcus phage P68 (virus)
#4: Protein/peptide inner core protein


Mass: 3507.314 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: Poly alanine chain fitted to the density of the inner core protein bound to hexon adjacent to portal
Source: (natural) Staphylococcus phage P68 (virus)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Staphylococcus phage P68 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 19.7 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus phage P68 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Staphylococcus aureus / Strain: dTarM 4220
Virus shellName: Capsid / Diameter: 480 nm / Triangulation number (T number): 4
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethaneTris1
210 mMcalcium chlorideCaCl1
310 mMsodium chlorideNaCl1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: blot time 2s; blot force -2; 3.6 ul of sample

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3 nm / Nominal defocus min: 1 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2891
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

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Processing

EM software
IDNameVersionCategory
1EMAN22.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.8.8model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
19PHENIXdev:3042model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 37218
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28826 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: The refinement was conducted on rigid body fitted major capsid proteins and Arstotzka proteins obtained from related structure of 6IAT; EMD-4438. The chains were fitted into hexon adjacent ...Details: The refinement was conducted on rigid body fitted major capsid proteins and Arstotzka proteins obtained from related structure of 6IAT; EMD-4438. The chains were fitted into hexon adjacent to portal of P68 capsid obtained from 5-fold symmetrized reconstruction. Subsequently, poly-alanine chains were manually built into densities corresponding to N-terminal part of head-fiber (chain IDs H,K,L) and C-terminal part of inner core protein (chain IDs X,Y,Z). The map was masked according to the related pdb in chimera, normalized and put into several rounds of a real space refinement in Phenix.
Atomic model buildingPDB-ID: 6IAT

6iat


Accession code: 6IAT / Source name: PDB / Type: experimental model

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